9LBT | pdb_00009lbt

DPPIV-VAMP

PDB DOI: https://doi.org/10.2210/pdb9LBT/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens, Cannabis sativa
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2025-01-03 Released: 2025-07-23
Deposition Author(s): Chen, H.H., Xing, X.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.195 (Depositor), 0.200 (DCC)
R-Value Work:
0.169 (Depositor), 0.173 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9LBT

This is version 1.0 of the entry. See complete history.

Literature

Discovery of an oral-admistrated biopeptide VAMP: a novel glucose homeostasis modulator with bifunctionalities of targeting intestinal DPP-IV and microbiota

Chen, H.H., Xing, X.H.

To be published.

Macromolecule Content

Total Structure Weight: 169.22 kDa
Atom Count: 13,431
Modeled Residue Count: 1,454
Deposited Residue Count: 1,460
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 soluble form	A, B	726	Homo sapiens	Mutation(s): 0 Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487 Go to UniProtKB: P27487
PHAROS: P27487 GTEx: ENSG00000197635
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27487
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VAL-ALA-MET-PRO	C, D	4	Cannabis sativa	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.195 (Depositor), 0.200 (DCC)
R-Value Work: 0.169 (Depositor), 0.173 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.827	α = 90
b = 126.37	β = 90
c = 136.867	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32101936

Revision History (Full details and data files)

Version 1.0: 2025-07-23
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.